RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

General features for molecule PDB_00724 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00724 Molecule name [?]: CRYSTAL STRUCTURE OF 2-AMINOPURINE LABELLED BACTERIAL DECODING SITE RNA Source [?]: RCSB Protein Data Bank Source ID [?]: 1T0D Reference [?]: S.SHANDRICK,Q.ZHAO,Q.HAN,B.K.AYIDA,M.TAKAHASHI, G.C.WINTERS,K.B.SIMONSEN,D.VOURLOUMIS,T.HERMANN. MONITORING MOLECULAR RECOGNITION OF THE RIBOSOMAL DECODING SITE.. ANGEW.CHEM.INT.ED.ENGL. V. 43 3177 2004 ASTM ACIEAY GE ISSN 0570-0833 Type [?]: Synthetic RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: SYNTHETIC Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 2.20 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 66 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 8 Number of paired bases [?]: 58

Click on any header below for additional features.

Stem features Number of stems [?]: 4 Number of base pairs in stems [?]: 29 Maximum length of a stem [?]: 8 Average length of a stem [?]: 7.25 Minimum length of a stem [?]: 7 Maximum estimated free energy [?]: -10 Average estimated free energy [?]: -12.6 Minimum estimated free energy [?]: -15.2

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 1 Average number of free bases in hairpin loops [?]: 1 Minimum number of free bases in hairpin loop [?]: 1

Bulge loop features Number of bulge loops [?]: 1 Maximum number of free bases in bulge loops [?]: 1 Average number of free bases in bulge loops [?]: 0.5 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 1 Maximum number of free bases in internal loops: 2 Average number of free bases in internal loops: 1.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 2

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 3 Total number of AG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 2

Pseudoknot features

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